Question: (Closed) Is there any specially designed software or a web service for the VCF file similarity search?
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genome21 • 10 wrote:
Is there any specially designed software or a web service for the VCF file similarity search, producing a report? Is there anything good beyond VCF compare commands in VCF, BCF tools, GATK?
This question doesn't contain enough information. Please specify which input you have (and how many samples) and which would be the desired output.
what's wrong/missing with those tools ?
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It depends on the reason you want to compare VCF files. What is the measure of similarity for you? In population analysis ADMIXTURE https://www.genetics.ucla.edu/software/admixture/ is one of the ways to cluster and then transform vcf files to vectors (called admixture vectors) and then compare these vectors. By admixture design vectors from within the same population will be closer.
If you want to find relatedness between two VCF samples you can look at the IBD with plink or use dedicated programs like KING to find kinship http://people.virginia.edu/~wc9c/KING/manual.html
Could you please specify your question?